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In January 2015, President Obama unveiled the Precision Medicine Initiative, an audacious research effort to revolutionize how we practice medicine and ultimately improve human health. Nearly one year later, US Vice President Joe Biden announced the $1 billion Moonshot to Cure Cancer, aiming to translate advances in genomics into treatments. To see these initiatives to fruition, we all need to work together to coordinate across silos and increase access to information.

Open access for sharing genomic data is not a new idea. The completion of the Human Genome Project and the 1000 Genomes Project showed us how the broad sharing of data generated by genomic research can maximize utility. At DNAnexus, we believe in fostering a culture of openness in genomic research to allow for medical breakthroughs. There are many troves of genomic data, but the mechanism for combining them is far from ideal.

Most data sharing in cancer genomics research has been centralized through rich, yet controlled-access databases like The Cancer Genome Atlas (TCGA) or International Cancer Genome Consortium (ICGC) –both of which properly approved researchers can easily access on the DNAnexus Platform. The access restrictions are structured with the worthy goal of protecting the privacy of individuals donating their samples and data to science, since access to genomic data could hypothetically lead to their re-identification. But arguably, by limiting the access to these datasets we are hampering faster progress and greater reach to patients.

Beyond the dataset itself, the pilot project’s salient contribution is the process developed for participant education and consent. Can cancer patients –with all the physical and psychological challenges they endure, and usually without extensive prior background in biology and genetic privacy– give truly informed consent for the benefits and risks of open-access data sharing? The rigorous protocol applied in this pilot indicates that many indeed possess the capacity, and the desire too.

Controlled-access research datasets will remain a reality and DNAnexus will continue our recognized leadership in cloud security and protection for both research and clinical applications. But the open-access TCRB cases –and, we hope, others like it to come– provide an opportunity for the research community to freely experiment with “real” cancer genomics data, rather than artificial simulations, and refine methods to better analyze controlled-access cases as well, ultimately advancing cancer research.

Our ASHG workshop session focused on this HGSC case study, with speakers Jeff Reid from Baylor College of Medicine and our own Andreas Sundquist and Andrew Carroll sharing some technical details about the project. We want to thank all of the scientists who packed the workshop room and offered us valuable feedback on their own cloud computing needs.

Separately, Jeff Reid spoke about the Mercury pipeline and DNAnexus in a program session called “Mo’ Data, Mo’ Problems.” Jeff’s talk was well received (blowing up the #ASHG2013 Twitter feed last Friday beginning at 9:48am EST) and sparked great discussion around the need for the scientific community to embrace a centralized environment to enable collaboration on biological questions rather than on building siloed computational infrastructure. During Q&A, one scientist asked Jeff if a pipeline for RNA-seq was in the works, and he said that an RNA-seq parallel to the Mercury pipeline is currently being developed to port on to DNAnexus for public use.

We also want to thank everyone who made our experience at ASHG so rewarding, including all the scientists who stopped by our booth — many of whom were drawn in by our new Genomics Cloud Computing Infographic visualizing the details of the Baylor HGSC case study. We had great conversations with our visitors and came away with useful intel about how our platform-as-a-service can support other genomics industry needs.

If you missed ASHG or have more questions about CHARGE and how the Mercury pipeline can help you, check out this use case or read related news reports from FierceBiotechIT or Genomeweb.

Mercury, designed by the Human Genome Sequencing Center at Baylor College of Medicine (HGSC), is used as the core variant-calling pipeline for the CHARGE consortium. The Mercury pipeline is a semi-automated and modular set of tools for the analysis of NGS data in clinically focused studies. HGSC designed the pipeline to identify mutations from genomic data, setting the stage for determining the significance of these mutations as a cause of serious disease.

Thanks to HGSC’s work with us, the Mercury pipeline is now freely available to any DNAnexus user. The Mercury pipeline is located in the applets folder of the HGSC_Mercury project. You can find the project, along with everything you need to run the applet, under the ‘Featured Projects’ section on your home page. Login to DNAnexus or create an account today to get started immediately.

Inside the Mercury Project

Both whole genome and exome samples

All annotation and reference data required

Pre–configured workflow (just drag & drop your inputs)

Results from the Mercury pipeline will be made up of a set of annotated variants from your data sample. You’ll also see all of the biologically significant data that applies to the variants from the Baylor College of Medicine database, using their Cassandra annotation tool. You can easily visualize the mappings and variant calls within our integrated genome browser.

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About DNAnexus

DNAnexus provides a global network for sharing and management of genomic data and tools to accelerate genomic medicine. The DNAnexus cloud-based platform is optimized to address the challenges of security, scalability, and collaboration, for organizations that are pursuing genomic-based approaches to health, in the clinic and in the research lab.

The DNAnexus team is made up of experts in computational biology and cloud computing who work with organizations to tackle some of the most exciting opportunities in human health, making it easier—and in many cases feasible—to work with genomic data. With DNAnexus, organizations can stay a step ahead in leveraging genomics to achieve their goals. The future of human health is in genomics. DNAnexus brings it all together.